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Added other Java processes with memory overhead, sorted alphabetically

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ameynert 2022-09-14 09:07:09 +01:00 committed by GitHub
parent 91ef9a3241
commit 9167e81214
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1 changed files with 52 additions and 34 deletions
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84
conf/pipeline/sarek/eddie.config
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@ -1,59 +1,77 @@
process { process {
withName:BWAMEM_MEM {
cpus = 16
memory = 128.GB
clusterOptions = {"-l h_vmem=${(task.memory + 8.GB).bytes/task.cpus}"}
}
withName:GATK4_CREATESEQUENCEDICTIONARY {
cpus = 1
clusterOptions = {"-l h_vmem=${(task.memory + 4.GB).bytes/task.cpus}"}
}
withName:LEARNREADORIENTATIONMODEL {
clusterOptions = {"-l h_vmem=${(task.memory + 4.GB).bytes/task.cpus}"}
}
withName:QUALIMAP_BAMQC {
cpus = 8
memory = 128.GB
clusterOptions = {"-l h_vmem=${(task.memory + 8.GB).bytes/task.cpus}"}
}
withName:GATK4_MARKDUPLICATES {
clusterOptions = {"-l h_vmem=${(task.memory + 4.GB).bytes/task.cpus}"}
}
withName:BASERECALIBRATOR {
clusterOptions = {"-l h_vmem=${(task.memory + 4.GB).bytes/task.cpus}"}
}
withName:APPLYBQSR { withName:APPLYBQSR {
clusterOptions = {"-l h_vmem=${(task.memory + 4.GB).bytes/task.cpus}"} clusterOptions = {"-l h_vmem=${(task.memory + 4.GB).bytes/task.cpus}"}
} }
withName:GATHERBQSRREPORTS { withName:APPLYBQSR_SPARK {
clusterOptions = {"-l h_vmem=${(task.memory + 4.GB).bytes/task.cpus}"} clusterOptions = {"-l h_vmem=${(task.memory + 4.GB).bytes/task.cpus}"}
} }
withName:GATK4_HAPLOTYPECALLER { withName:GATK4_APPLYVQSR {
clusterOptions = {"-l h_vmem=${(task.memory + 4.GB).bytes/task.cpus}"}
}
withName:GATK4_BASERECALIBRATOR {
clusterOptions = {"-l h_vmem=${(task.memory + 4.GB).bytes/task.cpus}"}
}
withName:GATK4_BASERECALIBRATOR_SPARK {
clusterOptions = {"-l h_vmem=${(task.memory + 4.GB).bytes/task.cpus}"}
}
withName:GATK4_CALCULATECONTAMINATION {
clusterOptions = {"-l h_vmem=${(task.memory + 4.GB).bytes/task.cpus}"}
}
withName:GATK4_CNNSCOREVARIANTS {
clusterOptions = {"-l h_vmem=${(task.memory + 4.GB).bytes/task.cpus}"}
}
withName:GATK4_CREATESEQUENCEDICTIONARY {
clusterOptions = {"-l h_vmem=${(task.memory + 4.GB).bytes/task.cpus}"}
}
withName:GATK4_ESTIMATELIBRARYCOMPLEXITY {
clusterOptions = {"-l h_vmem=${(task.memory + 4.GB).bytes/task.cpus}"}
}
withName:GATK4_FILTERMUTECTCALLS {
clusterOptions = {"-l h_vmem=${(task.memory + 4.GB).bytes/task.cpus}"}
}
withName:GATK4_FILTERVARIANTTRANCHES {
clusterOptions = {"-l h_vmem=${(task.memory + 4.GB).bytes/task.cpus}"}
}
withName:GATK4_GATHERBQSRREPORTS {
clusterOptions = {"-l h_vmem=${(task.memory + 4.GB).bytes/task.cpus}"}
}
withName:GATK4_GATHERPILEUPSUMMARIES {
clusterOptions = {"-l h_vmem=${(task.memory + 4.GB).bytes/task.cpus}"}
}
withName:GATK4_GENOMICSDBIMPORT {
clusterOptions = {"-l h_vmem=${(task.memory + 4.GB).bytes/task.cpus}"} clusterOptions = {"-l h_vmem=${(task.memory + 4.GB).bytes/task.cpus}"}
} }
withName:GATK4_GENOTYPEGVCFS { withName:GATK4_GENOTYPEGVCFS {
clusterOptions = {"-l h_vmem=${(task.memory + 4.GB).bytes/task.cpus}"} clusterOptions = {"-l h_vmem=${(task.memory + 4.GB).bytes/task.cpus}"}
} }
withName:MUTECT2 { withName:GATK4_GETPILEUPSUMMARIES {
clusterOptions = {"-l h_vmem=${(task.memory + 4.GB).bytes/task.cpus}"} clusterOptions = {"-l h_vmem=${(task.memory + 4.GB).bytes/task.cpus}"}
} }
withName:MERGE_MUTECT2 { withName:GATK4_HAPLOTYPECALLER {
clusterOptions = {"-l h_vmem=${(task.memory + 4.GB).bytes/task.cpus}"} clusterOptions = {"-l h_vmem=${(task.memory + 4.GB).bytes/task.cpus}"}
} }
withName:MERGEMUTECTSTATS { withName:GATK4_INTERVALLISTTOBED {
clusterOptions = {"-l h_vmem=${(task.memory + 4.GB).bytes/task.cpus}"} clusterOptions = {"-l h_vmem=${(task.memory + 4.GB).bytes/task.cpus}"}
} }
withName:GETPILEUPSUMMARIES { withName:GATK4_LEARNREADORIENTATIONMODEL {
clusterOptions = {"-l h_vmem=${(task.memory + 4.GB).bytes/task.cpus}"} clusterOptions = {"-l h_vmem=${(task.memory + 4.GB).bytes/task.cpus}"}
} }
withName:GATHERPILEUPSUMMARIES { withName:GATK4_MARKDUPLICATES {
clusterOptions = {"-l h_vmem=${(task.memory + 4.GB).bytes/task.cpus}"} clusterOptions = {"-l h_vmem=${(task.memory + 4.GB).bytes/task.cpus}"}
} }
withName:CALCULATECONTAMINATION { withName:GATK4_MARKDUPLICATES_SPARK {
clusterOptions = {"-l h_vmem=${(task.memory + 4.GB).bytes/task.cpus}"} clusterOptions = {"-l h_vmem=${(task.memory + 4.GB).bytes/task.cpus}"}
} }
withName:FILTERMUTECTCALLS { withName:GATK4_MERGEMUTECTSTATS {
clusterOptions = {"-l h_vmem=${(task.memory + 4.GB).bytes/task.cpus}"}
}
withName:GATK4_MERGEVCFS {
clusterOptions = {"-l h_vmem=${(task.memory + 4.GB).bytes/task.cpus}"}
}
withName:GATK4_MUTECT2 {
clusterOptions = {"-l h_vmem=${(task.memory + 4.GB).bytes/task.cpus}"}
}
withName:GATK4_VARIANTRECALIBRATOR {
clusterOptions = {"-l h_vmem=${(task.memory + 4.GB).bytes/task.cpus}"} clusterOptions = {"-l h_vmem=${(task.memory + 4.GB).bytes/task.cpus}"}
} }
} }